Nod2 (nucleotide-binding oligomerization domain containing 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Nod2 (nucleotide-binding oligomerization domain containing 2) Rattus norvegicus
Analyze
Symbol: Nod2
Name: nucleotide-binding oligomerization domain containing 2
RGD ID: 1306368
Description: Exhibits muramyl dipeptide binding activity. Involved in several processes, including cellular response to peptidoglycan; positive regulation of dendritic cell cytokine production; and response to muramyl dipeptide. Localizes to cytoplasm. Biomarker of colitis; middle cerebral artery infarction; and pancreatitis. Human ortholog(s) of this gene implicated in several diseases, including Blau syndrome; autoimmune disease (multiple); gastrointestinal carcinoma; intestinal disease (multiple); and lung disease (multiple). Orthologous to human NOD2 (nucleotide binding oligomerization domain containing 2); PARTICIPATES IN NOD-like receptor signaling pathway; nuclear factor kappa B signaling pathway; tuberculosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrobenzenesulfonic acid; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Card15; caspase recruitment domain family, member 15; LOC291912; nucleotide-binding oligomerization domain-containing protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,379,720 - 18,422,817 (-)NCBI
Rnor_6.0 Ensembl1919,332,594 - 19,377,492 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01919,342,061 - 19,389,366 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01930,375,065 - 30,409,527 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,662,337 - 19,697,341 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11919,670,606 - 19,715,845 (-)NCBI
Celera1918,269,940 - 18,304,004 (-)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acne  (ISO)
Acute Lung Injury  (IDA)
allergic rhinitis  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
autoimmune disease  (ISO)
Bacteremia  (ISO)
bacterial infectious disease  (ISO)
bacterial pneumonia  (ISO)
Behcet's disease  (ISO)
Blau syndrome  (ISO)
breast cancer  (ISO)
bronchiolitis obliterans  (ISO)
chronic obstructive pulmonary disease  (ISO)
colitis  (IEP,ISO)
Colonic Neoplasms  (ISO)
coronary artery disease  (ISO)
Crohn's disease  (ISO)
dermatitis  (ISO)
Experimental Arthritis  (ISO)
Experimental Colitis  (IEP)
familial Mediterranean fever  (ISO)
gastritis  (ISO)
gastrointestinal carcinoma  (ISO)
genetic disease  (ISO)
Graft vs Host Disease  (ISO)
Granuloma  (ISO)
hidradenitis suppurativa  (ISO)
inflammatory bowel disease  (ISO)
inflammatory bowel disease 1  (ISO,ISS)
intestinal disease  (ISO)
larynx cancer  (ISO)
Legionnaires' disease  (ISO)
leprosy  (ISO)
lung cancer  (ISO)
Lyme disease  (ISO)
meningococcal meningitis  (ISO)
Metaplasia  (ISO)
middle cerebral artery infarction  (IEP)
Ocular Toxoplasmosis  (ISO)
ovarian cancer  (ISO)
pancreatitis  (IEP)
perinatal necrotizing enterocolitis  (ISO)
PFAPA Syndrome  (ISO)
Pneumococcal Meningitis  (ISO)
pulmonary sarcoidosis  (ISO)
pulmonary tuberculosis  (ISO)
pyoderma gangrenosum  (ISO)
relapsing-remitting multiple sclerosis  (ISO)
Reperfusion Injury  (IEP)
rhinitis  (ISO)
Seasonal Allergic Rhinitis  (ISO)
Sepsis  (IEP,ISO)
Splenomegaly  (ISO)
Staphylococcal Pneumonia  (ISO)
systemic lupus erythematosus  (ISO)
transient cerebral ischemia  (ISO)
ulcerative colitis  (ISO)
uveitis  (ISO)
YAO SYNDROME  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of immune response  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to muramyl dipeptide  (ISO)
cellular response to organic cyclic compound  (IEP)
cellular response to peptidoglycan  (IEP,ISO)
defense response to bacterium  (IBA,ISO)
defense response to Gram-positive bacterium  (ISO)
detection of bacterium  (ISO)
detection of muramyl dipeptide  (ISO)
innate immune response  (ISO)
innate immune response in mucosa  (ISO)
intracellular signal transduction  (IBA,ISO)
maintenance of gastrointestinal epithelium  (ISO)
negative regulation of inflammatory response to antigenic stimulus  (ISO)
negative regulation of interferon-gamma production  (ISO)
negative regulation of interleukin-12 production  (ISO)
negative regulation of interleukin-18 production  (ISO)
negative regulation of interleukin-2 production  (ISO)
negative regulation of macrophage apoptotic process  (ISO)
negative regulation of NF-kappaB transcription factor activity  (ISO)
negative regulation of T cell mediated immunity  (ISO)
negative regulation of toll-like receptor 2 signaling pathway  (ISO)
negative regulation of tumor necrosis factor production  (ISO)
nucleotide-binding oligomerization domain containing 2 signaling pathway  (ISO)
pattern recognition receptor signaling pathway  (ISO)
positive regulation of antibacterial peptide biosynthetic process  (ISO)
positive regulation of B cell activation  (ISO)
positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria  (ISO)
positive regulation of cell population proliferation  (IDA)
positive regulation of cytokine production involved in immune response  (ISO)
positive regulation of cytokine production involved in inflammatory response  (ISO)
positive regulation of dendritic cell antigen processing and presentation  (ISO)
positive regulation of dendritic cell cytokine production  (IDA)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of humoral immune response mediated by circulating immunoglobulin  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IBA,ISO)
positive regulation of innate immune response  (ISO)
positive regulation of interleukin-1 beta production  (ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-17 production  (ISO)
positive regulation of interleukin-6 production  (ISO)
positive regulation of interleukin-8 production  (ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of MAP kinase activity  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of monocyte chemotactic protein-1 production  (ISO)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of nitric-oxide synthase biosynthetic process  (ISO)
positive regulation of Notch signaling pathway  (ISO)
positive regulation of oxidoreductase activity  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of phagocytosis  (ISO)
positive regulation of phosphatidylinositol 3-kinase activity  (ISO)
positive regulation of prostaglandin-E synthase activity  (ISO)
positive regulation of prostaglandin-endoperoxide synthase activity  (ISO)
positive regulation of protein K63-linked ubiquitination  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of stress-activated MAPK cascade  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
positive regulation of type 2 immune response  (ISO)
positive regulation of xenophagy  (ISO)
regulation of inflammatory response  (ISO)
regulation of neutrophil chemotaxis  (ISO)
response to exogenous dsRNA  (ISO)
response to lipopolysaccharide  (ISO)
response to muramyl dipeptide  (IBA,IDA,ISO)
response to nutrient  (IEP)
response to peptidoglycan  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Austin CM, etal., J Infect Dis. 2008 Jun 15;197(12):1713-6.
2. Bai X, etal., Neurochem Res. 2014 Aug;39(8):1405-15. doi: 10.1007/s11064-014-1326-y. Epub 2014 May 20.
3. Berkun Y, etal., Semin Arthritis Rheum. 2012 Aug;42(1):84-8. doi: 10.1016/j.semarthrit.2011.12.002. Epub 2012 Jan 12.
4. Berrington WR, etal., J Infect Dis. 2010 May 1;201(9):1422-35.
5. Biswas A, etal., Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14739-44. Epub 2010 Aug 2.
6. Correa-de-Santana E, etal., J Endocrinol. 2009 Oct;203(1):111-22. Epub 2009 Jul 16.
7. De Jager PL, etal., Genes Immun. 2006 Jun;7(4):327-34. Epub 2006 Apr 27.
8. Duan W, etal., J Allergy Clin Immunol. 2010 Dec;126(6):1284-93.e10. Epub 2010 Nov 4.
9. Dutra MS, etal., J Infect Dis. 2013 Jan 1;207(1):152-63. doi: 10.1093/infdis/jis640. Epub 2012 Oct 24.
10. Enevold C, etal., Mult Scler. 2010 Aug;16(8):942-9. doi: 10.1177/1352458510373264. Epub 2010 Jul 1.
11. Fernandez EM, etal., Gut. 2011 Aug;60(8):1050-9. Epub 2011 Apr 6.
12. Frutuoso MS, etal., Microbes Infect. 2010 Oct;12(11):819-27. Epub 2010 Jun 2.
13. Fujisawa M, etal., J Vet Med Sci. 2006 Jul;68(7):701-8.
14. Galluzzo S, etal., Hum Immunol. 2011 Aug;72(8):636-40. Epub 2011 Apr 29.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. Geddes K, etal., Infect Immun. 2010 Dec;78(12):5107-15. Epub 2010 Oct 4.
17. GOA data from the GO Consortium
18. Guo LH, etal., Biochem Biophys Res Commun. 2006 Oct 27;349(3):1156-62. Epub 2006 Sep 1.
19. Hagiwara S, etal., J Anesth. 2011 Feb;25(1):57-64. Epub 2010 Nov 6.
20. Hagiwara S, etal., Surg Today. 2010;40(2):137-45. Epub 2010 Jan 28.
21. Hildebrandt GC, etal., Biol Blood Marrow Transplant. 2008 Jan;14(1):67-74.
22. Hnatyszyn A, etal., Exp Mol Pathol. 2010 Jun;88(3):388-93. Epub 2010 Mar 15.
23. Holler E, etal., Blood. 2004 Aug 1;104(3):889-94. Epub 2004 Apr 15.
24. Hu S, etal., Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2013 Apr;27(8):393-6.
25. Hubert FX, etal., J Immunol. 2006 Jul 15;177(2):1007-16.
26. Hugot JP, etal., Nature. 2001 May 31;411(6837):599-603.
27. Kabesch M, etal., J Allergy Clin Immunol. 2003 Apr;111(4):813-7.
28. Kapetanovic R, etal., Microbes Infect. 2010 Sep;12(10):759-67. Epub 2010 May 21.
29. Kappen JH, etal., Rheumatology (Oxford). 2009 Nov;48(11):1375-7. doi: 10.1093/rheumatology/kep292. Epub 2009 Sep 11.
30. Kim YG, etal., Cell Host Microbe. 2011 Jun 16;9(6):496-507.
31. Kinose D, etal., Respirology. 2011 Sep 22. doi: 10.1111/j.1440-1843.2011.02069.x.
32. Lener MR, etal., Breast Cancer Res Treat. 2006 Jan;95(2):141-5.
33. Li H, etal., Eur J Pharmacol. 2010 Dec 15;649(1-3):92-9. Epub 2010 Sep 20.
34. Liu X, etal., BMC Infect Dis. 2014 Dec 2;14(1):648.
35. Lubinski J, etal., Hered Cancer Clin Pract. 2005 Mar 15;3(2):59-63.
36. Mahurkar S, etal., J Gastroenterol Hepatol. 2011 Apr;26(4):694-9. doi: 10.1111/j.1440-1746.2010.06533.x.
37. MGD data from the GO Consortium
38. Miceli-Richard C, etal., Nat Genet. 2001 Sep;29(1):19-20.
39. Natarajan C, etal., J Neuroimmunol. 2013 Dec 15;265(1-2):51-60. doi: 10.1016/j.jneuroim.2013.09.009. Epub 2013 Oct 9.
40. Okafuji I, etal., Arthritis Rheum. 2009 Jan;60(1):242-50. doi: 10.1002/art.24134.
41. OMIM Disease Annotation Pipeline
42. Opitz B, etal., J Biol Chem. 2004 Aug 27;279(35):36426-32. Epub 2004 Jun 23.
43. Osthoff M, etal., PLoS One. 2013 Sep 27;8(9):e76218. doi: 10.1371/journal.pone.0076218. eCollection 2013.
44. Packwood K, etal., Clin Exp Immunol. 2010 Sep;161(3):536-41. doi: 10.1111/j.1365-2249.2010.04216.x.
45. Peng Z, etal., Int Immunopharmacol. 2012 Aug;13(4):440-5. doi: 10.1016/j.intimp.2012.04.006. Epub 2012 May 7.
46. Petnicki-Ocwieja T, etal., PLoS One. 2011 Feb 28;6(2):e17414.
47. Pipeline to import KEGG annotations from KEGG into RGD
48. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
49. Qian M, etal., Pancreas. 2010 Oct;39(7):1034-40.
50. RGD automated data pipeline
51. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
52. RGD automated import pipeline for gene-chemical interactions
53. RGD comprehensive gene curation
54. Richardson WM, etal., Gastroenterology. 2010 Sep;139(3):904-17, 917.e1-6. doi: 10.1053/j.gastro.2010.05.038. Epub 2010 May 24.
55. Rivas MA, etal., Nat Genet. 2011 Oct 9. doi: 10.1038/ng.952.
56. Rose CD, etal., Arthritis Rheum. 2009 Jun;60(6):1797-803. doi: 10.1002/art.24533.
57. Rosenzweig HL, etal., Arthritis Rheum. 2010 Apr;62(4):1051-9. doi: 10.1002/art.27335.
58. Rosenzweig HL, etal., Inflamm Res. 2011 Jul;60(7):705-14. Epub 2011 Mar 20.
59. Rosenzweig HL, etal., Invest Ophthalmol Vis Sci. 2011 Jun 9;52(7):4106-12. Print 2011 Jun.
60. Sato H, etal., Eur Respir J. 2010 Feb;35(2):324-30. Epub 2009 Aug 13.
61. Shimada K, etal., PLoS Pathog. 2009 Apr;5(4):e1000379. Epub 2009 Apr 10.
62. Su Y, etal., J Neuropathol Exp Neurol. 2005 Nov;64(11):991-7.
63. Tang Q, etal., Zhongguo Zhong Yao Za Zhi. 2012 Jun;37(12):1814-7.
64. Tekin D, etal., Pediatr Crit Care Med. 2011 Mar 31.
65. Uyar FA, etal., Clin Exp Rheumatol. 2004 Jul-Aug;22(4 Suppl 34):S50-2.
66. van Duist MM, etal., Eur J Hum Genet. 2005 Jun;13(6):742-7.
67. van Well GT, etal., PLoS One. 2013 May 14;8(5):e64252. doi: 10.1371/journal.pone.0064252. Print 2013.
68. Weidinger S, etal., Clin Exp Allergy. 2005 Jul;35(7):866-72.
69. Xiao YT, etal., Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2013 Sep;25(9):527-32. doi: 10.3760/cma.j.issn.2095-4352.2013.09.005.
70. Yao Q, etal., Arthritis Res Ther. 2011;13(5):R148. doi: 10.1186/ar3462. Epub 2011 Sep 14.
71. Yu SL, etal., PLoS One. 2011;6(8):e23855. Epub 2011 Aug 19.
72. Yuan H, etal., Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):E5059-68. doi: 10.1073/pnas.1320862110. Epub 2013 Dec 9.
Additional References at PubMed
PMID:11087742   PMID:11385577   PMID:12527755   PMID:14560001   PMID:15075345   PMID:15107016   PMID:15220916   PMID:15620648   PMID:15653568   PMID:15692051   PMID:15753091   PMID:15998797  
PMID:16203728   PMID:16260731   PMID:16414084   PMID:16714539   PMID:16949315   PMID:17058067   PMID:17187069   PMID:17337451   PMID:17919942   PMID:17971865   PMID:18167348   PMID:18261938  
PMID:18511561   PMID:18855982   PMID:19139201   PMID:19218085   PMID:20008287   PMID:20441518   PMID:20844241   PMID:20926588   PMID:21040358   PMID:21156799   PMID:21172192   PMID:21887730  
PMID:22033934   PMID:23806334   PMID:23892723   PMID:24671169   PMID:24790089   PMID:25093298   PMID:25502289   PMID:25528059   PMID:25891078   PMID:25990971   PMID:26138652   PMID:27812135  
PMID:29303910   PMID:29913461   PMID:31649195  


Genomics

Comparative Map Data
Nod2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,379,720 - 18,422,817 (-)NCBI
Rnor_6.0 Ensembl1919,332,594 - 19,377,492 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01919,342,061 - 19,389,366 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01930,375,065 - 30,409,527 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,662,337 - 19,697,341 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11919,670,606 - 19,715,845 (-)NCBI
Celera1918,269,940 - 18,304,004 (-)NCBICelera
Cytogenetic Map19p11NCBI
NOD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1650,693,588 - 50,734,041 (+)EnsemblGRCh38hg38GRCh38
GRCh381650,693,587 - 50,733,077 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371650,727,517 - 50,766,986 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,288,551 - 49,324,488 (+)NCBINCBI36hg18NCBI36
Build 341649,288,550 - 49,324,488NCBI
Celera1635,246,377 - 35,282,313 (+)NCBI
Cytogenetic Map16q12.1NCBI
HuRef1636,618,016 - 36,653,950 (+)NCBIHuRef
CHM1_11652,138,579 - 52,174,514 (+)NCBICHM1_1
Nod2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,373,943 - 89,415,103 (+)NCBIGRCm39mm39
GRCm39 Ensembl889,373,943 - 89,415,102 (+)Ensembl
GRCm38888,647,315 - 88,688,474 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,647,315 - 88,688,474 (+)EnsemblGRCm38mm10GRCm38
MGSCv37891,171,246 - 91,212,373 (+)NCBIGRCm37mm9NCBIm37
MGSCv36891,537,452 - 91,578,579 (+)NCBImm8
Celera892,927,621 - 92,968,882 (+)NCBICelera
Cytogenetic Map8C3NCBI
Nod2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554338,746,004 - 8,782,710 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554338,746,213 - 8,780,119 (+)NCBIChiLan1.0ChiLan1.0
NOD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11649,834,385 - 49,873,783 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1649,837,891 - 49,873,773 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01630,955,976 - 30,995,451 (+)NCBIMhudiblu_PPA_v0panPan3
NOD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1264,636,850 - 64,667,232 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl264,635,519 - 64,667,232 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha261,209,788 - 61,240,085 (-)NCBI
ROS_Cfam_1.0265,182,339 - 65,218,538 (-)NCBI
UMICH_Zoey_3.1262,006,039 - 62,036,328 (-)NCBI
UNSW_CanFamBas_1.0263,025,931 - 63,056,292 (-)NCBI
UU_Cfam_GSD_1.0263,913,478 - 63,943,824 (-)NCBI
Nod2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934955,844,066 - 55,881,006 (-)NCBI
SpeTri2.0NW_0049364753,708,069 - 3,742,845 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl634,130,938 - 34,177,534 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1634,132,127 - 34,167,446 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NOD2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1536,492,158 - 36,531,766 (+)NCBI
ChlSab1.1 Ensembl536,496,414 - 36,530,499 (+)Ensembl
Vero_WHO_p1.0NW_02366604739,970,704 - 40,009,792 (-)NCBI
Nod2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247575,956,873 - 6,000,052 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124933090Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191073992926201726Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191529452433991703Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:83
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000065103
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1
Low 3 30 14 18 14 8 3 18 11
Below cutoff 27 23 23 23 8 11 66 32 21 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065103   ⟹   ENSRNOP00000061463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1919,332,594 - 19,376,789 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080964   ⟹   ENSRNOP00000073236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1919,334,619 - 19,377,492 (-)Ensembl
RefSeq Acc Id: NM_001106172   ⟹   NP_001099642
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,382,439 - 18,417,177 (-)NCBI
Rnor_6.01919,342,061 - 19,376,789 (-)NCBI
Rnor_5.01930,375,065 - 30,409,527 (-)NCBI
RGSC_v3.41919,662,337 - 19,697,341 (-)RGD
Celera1918,269,940 - 18,304,004 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772371   ⟹   XP_008770593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01919,343,174 - 19,382,301 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772372   ⟹   XP_008770594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01919,343,174 - 19,389,366 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772373   ⟹   XP_008770595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,395,441 - 18,422,817 (-)NCBI
Rnor_6.01919,343,174 - 19,382,301 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601207   ⟹   XP_017456696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01919,343,174 - 19,389,366 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097570   ⟹   XP_038953498
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,379,720 - 18,422,817 (-)NCBI
RefSeq Acc Id: XM_039097571   ⟹   XP_038953499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,399,888 - 18,422,817 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099642 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770595 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953498 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953499 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87529 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099642   ⟸   NM_001106172
- UniProtKB: D4A5W3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770594   ⟸   XM_008772372
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770593   ⟸   XM_008772371
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770595   ⟸   XM_008772373
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017456696   ⟸   XM_017601207
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000061463   ⟸   ENSRNOT00000065103
RefSeq Acc Id: ENSRNOP00000073236   ⟸   ENSRNOT00000080964
RefSeq Acc Id: XP_038953498   ⟸   XM_039097570
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953499   ⟸   XM_039097571
- Peptide Label: isoform X3
Protein Domains
CARD   NACHT

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 19686074 19686075 C T snv HCR/1Mco (UMich), LCR/2Mco (UMich), LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306368 AgrOrtholog
Ensembl Genes ENSRNOG00000014124 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061463 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073236 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065103 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080964 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro CARD UniProtKB/TrEMBL
  DEATH-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  NACHT_NTPase UniProtKB/TrEMBL
  NLRC_HD2 UniProtKB/TrEMBL
  NOD2_WH UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:291912 UniProtKB/TrEMBL
NCBI Gene 291912 ENTREZGENE
Pfam CARD UniProtKB/TrEMBL
  LRR_6 UniProtKB/TrEMBL
  NACHT UniProtKB/TrEMBL
  NLRC4_HD2 UniProtKB/TrEMBL
  NOD2_WH UniProtKB/TrEMBL
PharmGKB CARD15 RGD
PhenoGen Nod2 PhenoGen
PROSITE CARD UniProtKB/TrEMBL
  NACHT UniProtKB/TrEMBL
Superfamily-SCOP DEATH_like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2K4Z7_RAT UniProtKB/TrEMBL
  D4A5W3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-12-12 Nod2  nucleotide-binding oligomerization domain containing 2  Card15_predicted  caspase recruitment domain family, member 15 (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-01-12 Card15_predicted  caspase recruitment domain family, member 15 (predicted)      Symbol and Name status set to approved 70820 APPROVED